Publications

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Time-of-flight secondary ion mass spectrometry (TOF-SIMS) instruments are capable of saving an entire mass spectrum at each pixel of an image, allowing for retrospective analysis of masses that were not selected for analysis during data collection. These TOF-SIMS spectral images contain a wealth of information, but few tools are available to assist the analyst in visualizing the entire raw data set and as a result, most of the data are not analyzed. Automated, nonbiased, multivariate statistical analysis (MVSA) techniques are useful for converting the massive amount of data into a smaller number of chemical components (spectra and images) that are needed to fully describe the TOF-SIMS measurement. Many samples require two back-to-back TOF-SIMS measurements in order to fully characterize the sample, one measurement of the fraction of positively charged secondary ions (positive ion fraction) and one measurement of the fraction of negatively charged secondary ions (negative ion fraction). Each measurement then needs to be individually evaluated. In this paper, we report the first MVSA analysis of a concatenated TOF-SIMS date set comprising positive ion and negative ion spectral images collected on the same region of a sample. MVSA of concatenated data sets provides results that are intuitive and fully describe the sample. The analytical insight provided by MVSA of the concatenated data set was not obtained when either polarity data set was analyzed separately. © 2005 American Chemical Society.

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Spectral imaging where a complete spectrum is collected from each of a series of spatial locations (1D lines, 2D images or 3D volumes) is now available on a wide range of analytical tools - from electron and x-ray to ion beam instruments. With this capability to collect extremely large spectral images comes the need for automated data analysis tools that can rapidly and without bias reduce a large number of raw spectra to a compact, chemically relevant, and easily interpreted representation. It is clear that manual interrogation of individual spectra is impractical even for very small spectral images (< 5000 spectra). More typical spectral images can contain tens of thousands to millions of spectra, which given the constraint of acquisition time may contain between 5 and 300 counts per 1000-channel spectrum. Conventional manual approaches to spectral image analysis such as summing spectra from regions or constructing x-ray maps are prone to bias and possibly error. One way to comprehensively analyze spectral image data, which has been automated, is to utilize an unsupervised self-modeling multivariate statistical analysis method such as multivariate curve resolution (MCR). This approach has proven capable of solving a wide range of analytical problems based upon the counting of x-rays (SEM/STEM-EDX, XRF, PIXE), electrons (EELS, XPS) and ions (TOF-SIMS). As an example of the MCR approach, a STEM x-ray spectral image from a ZrB2-SiC composite was acquired and analyzed. The data were generated in a FEI Tecnai F30-ST TEM/STEM operated at 300kV, equipped with an EDAX SUTW x-ray detector. The spectral image was acquired with the TIA software on the STEM at 128 by 128 pixels (12nm/pixel) for 100msec dwell per pixel (total acquisition time was 30 minutes) with a probe of approximately the same size as each pixel. Each spectrum in the image had, on average, 500 counts. The calculation took 5 seconds on a PC workstation with dual 2.4GHz PentiumIV Xeon processors and 2Gbytes of RAM and resulted in four chemically relevant components, which are shown in Figure 1. The analysis region was at a triple junction of three ZrB2 grains that contained zirconium oxide, aluminum oxide and a glass phase. The power of unbiased statistical methods, such as MCR as applied here, is that no a priori knowledge of the material's chemistry is required. The algorithms, in this case, effectively reduced over 16,000 2000-channel spectra (64Mbytes) to four images and four spectral shapes (72kbytes), which in this case represent chemical phases. This three order of magnitude compression is achieved rapidly with no loss of chemical information. There is also the potential to correlate multiple analytical techniques like, for example, EELS and EDS in the STEM adding sensitivity to light elements as well as bonding information for EELS to the more comprehensive spectral coverage of EDS.

Microanalysis is typically performed to analyze the near surface of materials. There are many instances where chemical information about the third spatial dimension is essential to the solution of materials analyses. The majority of 3D analyses however focus on limited spectral acquisition and/or analysis. For truly comprehensive 3D chemical characterization, 4D spectral images (a complete spectrum from each volume element of a region of a specimen) are needed. Furthermore, a robust statistical method is needed to extract the maximum amount of chemical information from that extremely large amount of data. In this paper, an example of the acquisition and multivariate statistical analysis of 4D (3-spatial and 1-spectral dimension) x-ray spectral images is described. The method of utilizing a single- or dual-beam FIB (w/o or w/SEM) to get at 3D chemistry has been described by others with respect to secondary-ion mass spectrometry. The basic methodology described in those works has been modified for comprehensive x-ray microanalysis in a dual-beam FIB/SEM (FEI Co. DB-235). In brief, the FIB is used to serially section a site-specific region of a sample and then the electron beam is rastered over the exposed surfaces with x-ray spectral images being acquired at each section. All this is performed without rotating or tilting the specimen between FIB cutting and SEM imaging/x-ray spectral image acquisition. The resultant 4D spectral image is then unfolded (number of volume elements by number of channels) and subjected to the same multivariate curve resolution (MCR) approach that has proven successful for the analysis of lower-dimension x-ray spectral images. The TSI data sets can be in excess of 4Gbytes. This problem has been overcome (for now) and images up to 6Gbytes have been analyzed in this work. The method for analyzing such large spectral images will be described in this presentation. A comprehensive 3D chemical analysis was performed on several corrosion specimens of Cu electroplated with various metals. Figure 1A shows the top view of the localized corrosion region prepared for FIB sectioning. The TSI region has been coated with Pt and a trench has been milled along the bottom edge of the region, exposing it to the electron beam as seen in Figure 1B. The TSI consisted of 25 sections and was approximately 6Gbytes. Figure 1C shows several of the components rendered in 3D: Green is Cu; blue is Pb; cyan represents one of the corrosion products that contains Cu, Zn, O, S, and C; and orange represents the other corrosion product with Zn, O, S and C. Figure 1 D shows all of the component spectral shapes from the analysis. There is severe pathological overlap of the spectra from Ni, Cu and Zn as well as Pb and S. in spite of this clean spectral shapes have been extracted from the TSI. This powerful TSI technique could be applied to other sectioning methods well.

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While hyperspectral imaging systems are increasingly used in remote sensing and offer enhanced scene characterization relative to univariate and multispectral technologies, it has proven difficult in practice to extract all of the useful information from these systems due to overwhelming data volume, confounding atmospheric effects, and the limited a priori knowledge regarding the scene. The need exists for the ability to perform rapid and comprehensive data exploitation of remotely sensed hyperspectral imagery. To address this need, this paper describes the application of a fast and rigorous multivariate curve resolution (MCR) algorithm to remotely sensed thermal infrared hyperspectral images. Employing minimal a priori knowledge, notably non-negativity constraints on the extracted endmember profiles and a constant abundance constraint for the atmospheric upwelling component, it is demonstrated that MCR can successfully compensate thermal infrared hyperspectral images for atmospheric upwelling and, thereby, transmittance effects. We take a semi-synthetic approach to obtaining image data containing gas plumes by adding emission gas signals onto real hyperspectral images. MCR can accurately estimate the relative spectral absorption coefficients and thermal contrast distribution of an ammonia gas plume component added near the minimum detectable quantity.

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Analytical instrumentation such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides a tremendous quantity of data since an entire mass spectrum is saved at each pixel in an ion image. The analyst often selects only a few species for detailed analysis; the majority of the data are not utilized. Researchers at Sandia National Laboratory (SNL) have developed a powerful multivariate statistical analysis (MVSA) toolkit named AXSIA (Automated eXpert Spectrum Image Analysis) that looks for trends in complete datasets (e.g., analyzes the entire mass spectrum at each pixel). A unique feature of the AXSIA toolkit is the generation of intuitive results (e.g., negative peaks are not allowed in the spectral response). The robust statistical process is able to unambiguously identify all of the spectral features uniquely associated with each distinct component throughout the dataset. General Electric and Sandia used AXSIA to analyze raw data files generated on an Ion Tof IV ToF-SIMS instrument. Here, we will show that the MVSA toolkit identified metallic contaminants within a defect in a polymer sample. These metallic contaminants were not identifiable using standard data analysis protocol. © 2004 Elsevier B.V. All rights reserved.

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is capable of generating huge volumes of data. TOF-SIMS spectrum-images, comprising complete mass spectra at each point in a spatial array, are easily acquired with modern instrumentation. With the addition of depth profiling, spectra can be collected from up to three spatial dimensions leading to data sets that are seemingly unlimited in size. Multivariate statistical techniques such as principal component analysis, multivariate curve resolution and other factor analysis methods are being used to meet the challenge of turning that mountain of data into analytically useful knowledge. These methods work by extracting the essential chemical information embedded in the high dimensional data into a limited number of factors that describe the spectrally active pure components present in the sample. A review of the recent literature shows that the mass spectral data are often scaled prior to multivariate analysis. Common preprocessing steps include normalization of the pixel intensities, and auto- or variance-scaling of the mass spectra. In this paper, we will demonstrate that these pretreatments can lead to less than satisfactory results and, in fact, can be counterproductive. By taking the Poisson nature of the data into consideration, however, a scaling method can be devised that is optimal in a maximum likelihood sense. Using a simple and intuitive example, we will demonstrate the superiority of the optimal scaling approach for estimating the number of pure components, for segregating the chemical information into as few components as possible, and for discriminating small features from noise. © 2004 Elsevier B.V. All rights reserved.

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) by its parallel nature, generates complex and very large datasets quickly and easily. An example of such a large dataset is a spectral image where a complete spectrum is collected for each pixel. Unfortunately, the large size of the data matrix involved makes it difficult to extract the chemical information from the data using traditional techniques. Because time constraints prevent an analysis of every peak, prior knowledge is used to select the most probable and significant peaks for evaluation. However, this approach may lead to a misinterpretation of the system under analysis. Ideally, the complete spectral image would be used to provide a comprehensive, unbiased materials characterization based on full spectral signatures. Automated eXpert spectral image analysis (AXSIA) software developed at Sandia National Laboratories implements a multivariate curve resolution technique that was originally developed for energy dispersive X-ray spectroscopy (EDS) [Microsci. Microanal. 9 (2003) 1]. This paper will demonstrate the application of the method to TOF-SIMS. AXSIA distills complex and very large spectral image datasets into a limited number of physically realizable and easily interpretable chemical components, including both spectra and concentrations. The number of components derived during the analysis represents the minimum number of components needed to completely describe the chemical information in the original dataset. Since full spectral signatures are used to determine each component, an enhanced signal-to-noise is realized. The efficient statistical aggregation of chemical information enables small and unexpected features to be automatically found without user intervention. © 2004 Elsevier B.V. All rights reserved.

Algorithms for multivariate image analysis and other large-scale applications of multivariate curve resolution (MCR) typically employ constrained alternating least squares (ALS) procedures in their solution. The solution to a least squares problem under general linear equality and inequality constraints can be reduced to the solution of a non-negativity-constrained least squares (NNLS) problem. Thus the efficiency of the solution to any constrained least square problem rests heavily on the underlying NNLS algorithm. We present a new NNLS solution algorithm that is appropriate to large-scale MCR and other ALS applications. Our new algorithm rearranges the calculations in the standard active set NNLS method on the basis of combinatorial reasoning. This rearrangement serves to reduce substantially the computational burden required for NNLS problems having large numbers of observation vectors.

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High throughput instruments and analysis techniques are required in order to make good use of the genomic sequences that have recently become available for many species, including humans. These instruments and methods must work with tens of thousands of genes simultaneously, and must be able to identify the small subsets of those genes that are implicated in the observed phenotypes, or, for instance, in responses to therapies. Microarrays represent one such high throughput method, which continue to find increasingly broad application. This project has improved microarray technology in several important areas. First, we developed the hyperspectral scanner, which has discovered and diagnosed numerous flaws in techniques broadly employed by microarray researchers. Second, we used a series of statistically designed experiments to identify and correct errors in our microarray data to dramatically improve the accuracy, precision, and repeatability of the microarray gene expression data. Third, our research developed new informatics techniques to identify genes with significantly different expression levels. Finally, natural language processing techniques were applied to improve our ability to make use of online literature annotating the important genes. In combination, this research has improved the reliability and precision of laboratory methods and instruments, while also enabling substantially faster analysis and discovery.

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Energy dispersive x-ray (EDX) spectrum imaging has been performed in a scanning electron microscope (SEM) on a metal/ceramic braze to characterize the elemental distribution near the interface. Statistical methods were utilized to extract the relevant information (i.e., chemical phases and their distributions) from the spectrum image data set in a robust and unbiased way. The raw spectrum image was over 15 Mbytes (7500 spectra) while the statistical analysis resulted in five spectra and five images which describe the phases resolved above the noise level and their distribution in the microstructure.